LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
  using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent

units           lj
atom_style      line
dimension       2

read_data       data.line
Reading data file ...
  orthogonal box = (-22.553882 -22.553882 -0.5) to (22.553882 22.553882 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  350 atoms
  350 lines
  read_data CPU = 0.003 seconds

velocity        all create 1.44 320984 loop geom

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes
neigh_modify    exclude molecule/intra all

pair_style      line/lj 2.5
pair_coeff      * * 0.25 0.25 1.0 0.25 2.5

fix             2 all rigid molecule langevin 2.0 2.0 1.0 492983
  100 rigid bodies with 350 atoms

fix             3 all deform 5 x scale 0.8 y scale 0.8
fix             4 all enforce2d

compute         10 all property/atom end1x end1y end2x end2y

#dump           1 all custom 500 dump1.atom id type x y z ix iy iz
#dump           2 all custom 500 dump1.line id type #               c_10[1] c_10[2] c_10[3] c_10[4]

timestep        0.001

compute         1 all erotate/asphere
compute         2 all ke
compute         3 all pe
variable        toteng equal (c_1+c_2+c_3)/atoms

compute_modify  thermo_temp extra/dof -350

thermo          1000
thermo_style    custom step f_2 pe ke c_1 c_2 c_3 v_toteng

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419

@Article{Gissinger24,
 author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
 title = {Type Label Framework for Bonded Force Fields in LAMMPS},
 journal = {J. Phys. Chem. B},
 year =    2024,
 volume =  128,
 number =  13,
 pages =   {3282–-3297}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 33 33 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair line/lj, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.742 | 4.742 | 4.742 Mbytes
   Step          f_2           PotEng         KinEng          c_1            c_2            c_3          v_toteng   
         0   1.1872976      0              0.46543528     0.03617212     0.46543528     0              0.5016074    
      1000   1.9084412     -0.001043719    0.71003395     0.089891202    0.71003395    -0.001043719    0.79888143   
      2000   2.31668       -0.020711665    0.83611544     0.13062287     0.83611544    -0.020711665    0.94602664   
      3000   2.3094506     -0.062018072    0.80584123     0.15326943     0.80584123    -0.062018072    0.8970926    
      4000   2.4383442     -0.053659995    0.86864073     0.14696993     0.86864073    -0.053659995    0.96195067   
      5000   2.5885917     -0.15612821     0.90351683     0.17156633     0.90351683    -0.15612821     0.91895495   
      6000   2.1187379     -0.072041135    0.76933527     0.11557939     0.76933527    -0.072041135    0.81287353   
      7000   2.1407592     -0.057727294    0.75154343     0.13827066     0.75154343    -0.057727294    0.8320868    
      8000   2.0661844     -0.097529608    0.71093839     0.14547433     0.71093839    -0.097529608    0.75888311   
      9000   2.1574445     -0.052890857    0.78826145     0.11363136     0.78826145    -0.052890857    0.84900195   
     10000   2.473097      -0.092376489    0.85756337     0.16861278     0.85756337    -0.092376489    0.93379965   
Loop time of 1.16704 on 1 procs for 10000 steps with 350 atoms

Performance: 740334.372 tau/day, 8568.685 timesteps/s, 2.999 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.80757    | 0.80757    | 0.80757    |   0.0 | 69.20
Neigh   | 0.0090046  | 0.0090046  | 0.0090046  |   0.0 |  0.77
Comm    | 0.011808   | 0.011808   | 0.011808   |   0.0 |  1.01
Output  | 0.000194   | 0.000194   | 0.000194   |   0.0 |  0.02
Modify  | 0.3317     | 0.3317     | 0.3317     |   0.0 | 28.42
Other   |            | 0.006768   |            |       |  0.58

Nlocal:            350 ave         350 max         350 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            101 ave         101 max         101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            853 ave         853 max         853 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 853
Ave neighs/atom = 2.4371429
Neighbor list builds = 274
Dangerous builds = 0

#undump          1
#undump          2
unfix           3

change_box      all triclinic
Changing box ...
  triclinic box = (-18.043106 -18.043106 -0.5) to (18.043106 18.043106 0.5) with tilt (0 0 0)

#dump           1 all custom 500 dump2.atom id type x y z ix iy iz
#dump           2 all custom 500 dump2.line id type #               c_10[1] c_10[2] c_10[3] c_10[4]

fix             3 all deform 1 xy erate 0.01 units box

run             10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 26 26 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair line/lj, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton/tri
      stencil: half/bin/2d/tri
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.756 | 4.756 | 4.756 Mbytes
   Step          f_2           PotEng         KinEng          c_1            c_2            c_3          v_toteng   
     10000   2.473097      -0.092380532    0.85753671     0.16863499     0.85753671    -0.092380532    0.93379117   
     11000   2.5185915     -0.1015737      0.84230876     0.197573       0.84230876    -0.1015737      0.93830806   
     12000   2.5971728     -0.13087195     0.90608898     0.17248755     0.90608898    -0.13087195     0.94770458   
     13000   2.5065714     -0.14666584     0.83804307     0.19683483     0.83804307    -0.14666584     0.88821206   
     14000   2.1672357     -0.10720878     0.79713452     0.10973398     0.79713452    -0.10720878     0.79965972   
     15000   2.3444438     -0.14780285     0.81642139     0.15695019     0.81642139    -0.14780285     0.82556873   
     16000   2.2672973     -0.12590007     0.76672668     0.17081014     0.76672668    -0.12590007     0.81163675   
     17000   2.3999651     -0.15464102     0.85708567     0.14289234     0.85708567    -0.15464102     0.84533699   
     18000   2.2024356     -0.14077779     0.76727873     0.14718521     0.76727873    -0.14077779     0.77368615   
     19000   2.5411572     -0.092014576    0.85750101     0.19297197     0.85750101    -0.092014576    0.95845841   
     20000   2.2113691     -0.11944862     0.77295445     0.14564597     0.77295445    -0.11944862     0.79915181   
Loop time of 1.76388 on 1 procs for 10000 steps with 350 atoms

Performance: 489827.896 tau/day, 5669.304 timesteps/s, 1.984 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.3668     | 1.3668     | 1.3668     |   0.0 | 77.49
Neigh   | 0.018849   | 0.018849   | 0.018849   |   0.0 |  1.07
Comm    | 0.013338   | 0.013338   | 0.013338   |   0.0 |  0.76
Output  | 0.00020434 | 0.00020434 | 0.00020434 |   0.0 |  0.01
Modify  | 0.35698    | 0.35698    | 0.35698    |   0.0 | 20.24
Other   |            | 0.007667   |            |       |  0.43

Nlocal:            350 ave         350 max         350 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            119 ave         119 max         119 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            997 ave         997 max         997 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 997
Ave neighs/atom = 2.8485714
Neighbor list builds = 283
Dangerous builds = 0
Total wall time: 0:00:02
